Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection

Abstract

Most human immunodeficiency virus type 1 (HIV-1)-infected individuals develop an HIV-specific neutralizing antibody (NAb) response that selects for escape variants of the virus. Here, we studied autologous NAb responses in five typical CCR5-using progressors in relation to viral NAb escape and molecular changes in the viral envelope (Env) in the period from seroconversion until after AIDS diagnosis. In sera from three patients, high-titer neutralizing activity was observed against the earliest autologous virus variants, followed by declining humoral immune responses against subsequent viral escape variants. Autologous neutralizing activity was undetectable in sera from two patients. Patients with high-titer neutralizing activity in serum showed the strongest positive selection pressure on Env early in infection. In the initial phase of infection, gp160 length and the number of potential N-linked glycosylation sites (PNGS) increased in viruses from all patients. Over the course of infection, positive selection pressure declined as the NAb response subsided, coinciding with reversions of changes in gp160 length and the number of PNGS. A number of identical amino acid changes were observed over the course of infection in the viral quasispecies of different patients. Our results indicate that although neutralizing autologous humoral immunity may have a limited effect on the disease course, it is an important selection pressure in virus evolution early in infection, while declining HIV-specific humoral immunity in later stages may coincide with reversion of NAb-driven changes in Env.

FIG. 1.

CD4⁺ T-cell numbers, viral loads, and antiretroviral treatments of five typical R5 progressors from the ACS. All patients had an asymptomatic follow-up of 7 to 11 years between SC and clinical AIDS diagnosis. The length and type of antiretroviral therapy are indicated at the top of each diagram.

FIG. 2.

Development of autologous humoral immune responses. Average IC₅₀s, determined by linear regression, of ≤5 virus variants per time point are indicated. Bars with identical shading represent inhibition of virus isolates from one time point by sera from different time points (as indicated on the x axis). The dashed lines represent background measurements using pooled sera from uninfected individuals. Note that the maximum value on the y axis in the graph for patient H1 is higher than the others. mo, months.

FIG. 3.

Longitudinal analysis of changes in gp160 length and number of PNGS. Each dot represents one clonal virus variant. The horizontal bars indicate average values per time point. P values were calculated using a t test for independent samples. (A) Length of gp160. (B) Number of PNGS in gp160.

FIG. 4.

Longitudinal analysis of changes in the number of PNGS in the constant and variable regions of gp120. Each dot in the graphs indicates the characteristics of one clonal virus variant. The horizontal bars indicate the averages per time point. P values were calculated using a t test for independent samples. (A) Number of PNGS in the constant regions of gp120. (B) Number of PNGS in the variable regions of gp120.

FIG. 5.

Changes in the locations of PNGS in gp160 sequences over the course of infection. The percentage of viruses with a PNGS at a given position per patient per time point is color coded using increasingly darker shades of gray for the constant regions of gp120 and gp41 and increasingly darker shades of red, blue, yellow, purple, and green for the V1, V2, V3, V4, and V5 regions, respectively. Mo, months.

FIG. 5.

Changes in the locations of PNGS in gp160 sequences over the course of infection. The percentage of viruses with a PNGS at a given position per patient per time point is color coded using increasingly darker shades of gray for the constant regions of gp120 and gp41 and increasingly darker shades of red, blue, yellow, purple, and green for the V1, V2, V3, V4, and V5 regions, respectively. Mo, months.

FIG. 6.

dN and dS rates in env during the course of infection. (A) Selection pressure on Env, expressed as the ratio between dN and dS. Ratios are shown for full-length gp160, gp41, and gp120 and constant regions and variable regions of gp120 between viruses from successive time points. The dashed lines indicate a dN/dS ratio of 1.0. dN/dS ratios of >1.0 are indicative of positive selection. (B) Divergence of dN and dS over the course of infection relative to the virus population present shortly after SC (time point I in panel A). For all patients, time point V corresponds to the moment of clinical AIDS diagnosis.